Chuck vs The Intersect 3
by Werter
Summary: Takes place a few months after the season 3 finale. The Buy More has been rebuilt, he has taken on his position as Orion, and has still quit the spy life...for now. Full summary inside.
1. Chuck vs the TeenSpy

Summary: Everything in Chuck Bartowski's life is about to change. What do a teenage boy, Daniel Shaw, a mysterious organization, and "Magic," all have in common? The Intersect 3.0

Disclaimer: *Sigh* Alas, I do not own Chuck :(

Chapter 1: Chuck vs the TeenSpy

Chuck Bartowski, ex-secret agent, senior supervisor of the Burbank Buy More Nerd Herd, current Orion, etc. sat behind the Nerd Herd reception desk. He was reading the latest copy of _GameSpy_ Magazine, when a boy around the age of 15 walked up to the desk holding an iPhone 4.

"Hello there young man, my name is Chuck, how can I help you today?" Chuck asked hoping for a chance to mess with the new iPhone.

"Hi, you see, my computer's down, I was wondering if you could help me set up my new iPhone?" asked the teenager.

"Oh,sure," said Chuck as the boy hands him the phone, "just let me plug it here…There we go, did you know that with some tweaking, the core processor of the iPhone 4 could be made to run the real Mac OS X Leopard?" asks Chuck Confidently.

"No, I didn't, that's awesome!" said the teenager, genuienly intrigued.

"Yeah, it is pretty cool if I do say so my self." said a rather confident Chuck. He turns on the phone, admiring the retina display. After a few minutes, Chuck had the phone ready for the teen's information.

"Name?" begins Chuck.

"Sam Williams" replies the teenager.

_A Plane_

_Several images of Sam Williams' different passports._

_A record of CIA recruitment by Langston Graham_

_A list of the projects he was invovled in, most being marked Above Top Secret_

_The Words: PROJECT BLACKWOOD_

_A Plane_

Chuck blinks several times, recovering from his flash.1

"Hello? Are you okay?" the Teenager asked, concerned.

Chuck blinks twice, looking at the teenager in astonshiment.

"Did you just flash?" asks the teenager.

"H-How…?" said Chuck.

"Trust me, Chuck, I know a lot of things." Said the teenager.

Chuck, out of both sudden fear and desperation, pushed the silent alarm under his desk. Seconds later, Chuck saw his girlfriend, Sarah, approach behind the teenager, amd put a gun to his back, careful not to let anyone see.

"Just walk out slowly, and you won't get hurt." said Sarah.

"Ahhh…Agent Walker, so nice to finally make your acquaintance," said the teenager. She pushes the muzzle harder into his back.

"I said, move it!" said Sarah, anger rising in her voice.

"Alright, alright, I'm moving!" said the teenager with a cocky smile.

…...

The whole team had gathered in castle, Chuck, Sarah, Casey, and even Morgan, were situated in Castle's main room. Sam had been deposited in one of the detention areas. Suddenly, Beckman appeared on the screen, looking slightly panicked.

"I'm sorry to have to tell you like this, but it's a good thing you contacted me about Agent Williams," said the General.

"Why's that?" asks Chuck.

"Because, _Mr. _Bartowski, Agent Williams shouldn't be anywhere near Los Angeles. My Records indicate he should be in Puerto Rico." said the General.

"General, if I may be so bold, can I ask how a teenager became a spy for the CIA?" asks Morgan.

"I'm afraid that's above all of your ranks, Agent Grimes." said the General.

"Its okay, you can tell them," said a voice from behind them. Every one jumps, and those who have a gun, point it at the source of the voice. Out of the shadows emerges Agent Williams.

"How did you get out?" grunts Casey.

"I helped design Castle, and, as if that wasn't enough, I Flashed." Said Sam.

"Y-You what?" asks Sarah.

"I Flashed, you see, I'm an Inter-"he began.

"Agent Williams!" shouted Beckman."That is above their clearance!"

"First off General, that's 'Sir' or 'Special Agent' but not just Agent: Second, it's my file, and I will share it with who I want to!" said Sam.

"Yes… sir" said a defeated General Beckman.

"Now where was I?"said Sam," Ahhh, yes I'm an Intersect. Before you ask how, let me tell you, I built one. Yes, Chuck, your dad was technically the only one who could build one, because according to the US Government, I don't exist."

"How is this all possible? I mean, I still don't see why the CIA would want to recruit you." Said Chuck.

"Well, it's probably because I can do this," said Sam, reaching his hand out. To Chuck's surprise, a pen materialized in his hand.

"Whoa!" said Morgan.

Chuck was about to comment on it,when he suddenly flashed. It wasn't a regular 2.0 flash. Instead of being orange, it was a light green, with strange symbols flying through his vision. The flash ended, Chuck pushed his hand out and a tranq pistol appeared in his hand.

"Whoa, Chuck!" exasperated Morgan. Casey and Sarah just stared in awe.

"It worked!" said Sam, with a cocky grin.

"What worked?" piped in the General.

"Oh, right," said Sam, "I forget to mention, Chuck, about the intersect, it-" He was cut off by the sound of an alarm, and the words PERIMETER BREACH, flashing on all the screens.

"Oh crap," said Casey, running to the nearest computer.

"Who is it, the Ring?" asked Sarah.

But before anyone else could answer, Sam spoke,"No, it's something much worse." As soon as he finished saying it, the main door to castle slid open and a a small black container was flung into the room, spewing smoke in all directions. The last thing he said before everyone fainted was this. "_Shadow Troopers."_

And with that, everything went dark…


	2. Chuck vs Shaw

Chapter 2: Chuck vs Shaw.

Chuck awoke to smell of salt. He looked around the room and found himself unable to move his head or body. He looked down at himself and saw he was in a chair that he was oddly similar to the one that Fulcrum had him in when he was to receive Fulcrum's Dark Intersect. He looked to right and saw Sarah strapped to another chair, to his left, Morgan. Casey was next to Morgan, and Sam was next to Sarah, while Sam's Chair was also attached to Casey's making a circle. Chuck noticed the room was all white, and the walls and floors were made of a bunch of screens, similar to the Intersect room.

"Sarah! Sarah, are you okay?" Chuck asked.

'Yeah, I'm fine, how about you?" she asked.

"I'm good, how about Mor- " said Chuck

"I'm fine, buddy," interrupted Morgan, "Wow, what a James Bond situation we've got ourselves into here, huh?"

"We're fine too, thanks for asking!" said Casey with a grunt, from behind Chuck.

As Chuck was about to speak, all of the TV's in the Room turned on, and the face of Daniel Shaw appeared.

"Hello Chuck. How are you? Nice and Cozy?" he said, a cocky smile on his face, "You see, you're here for a test, an extremely dangerous test. The SMF has finally completed an Intersect, and we're gonna test it, on all of you. It could kill you, but that's why were testing it on _you_ first! Good luck...not really."

The screens flashed, then went black, replacing Shaw's face with a countdown.

"The Test will begin in 10 seconds." Said a female voice. The platform the chairs were on began to spin.

"Guys, if you can, close your eyes!" shouted Chuck.

"5…4…3…2…1..Beginning Test." Counted the voice. All of the screens turned on, flashing various images on the screen. The chairs continued to spin, gaining speed, until the screens were a blur of colors. As time went on, Chuck's head began to throb.

After about an hour, Chuck's brain began to feel like mush. He felt the chair begin to slow down, and he quickly passed out.

Chuck awoke on a small cot bed. He instantly shot his hands to his temples as he had an extreme headache. The images were still burned into his eyes, he could still see them flashing before him. Chuck shook his head, trying to get ride of the images.

As Chuck's vision cleared, he sat up and examined the room he was in. The room was empty, aside from a small computer monitor on the wall, a security camera, and the bed he was sitting on. On the wall there was some strange symbol, with the letters SMF written over it.

_A Spaceship_

_A Picture of a large, futuristic building_

_Recordings of various training exercises_

_Futuristic weapons_

_More training exercises_

_A picture of Daniel Shaw shaking hands with the CEO of the SMF, Christopher Felkin_

_A Spaceship_

Then, it happened again. Chuck heard a loud screeching sound, and felt extreme pain in his head, as random images flashed before his eyes, scratching his vision. He was barely able to think, but felt his wrist with one hand, while groaning in pain. The Governor, it was gone! Chuck cradled his head in his hands. After a few more seconds, the pain stopped.

Moments later, the door opened up, and in walked Daniel Shaw. Shaw was wearing a tuxedo, and on his wrist was… the Governor! _His Governor._

"Good Morning Chuck, sleep well I hope?" said Shaw, as if they were best friends.

"You!" screamed Chuck ramming at Shaw, who stepped to the side, causing Chuck to slam into the wall. He then grabbed Chuck by the collar and slammed him into the wall, and punched him in the gut. Chuck moaned in pain.

"That's for beating me last time!" said Shaw, he punched him again, "That's for taking Sarah from me," he punched again, "That's for making me lose my job!" he punched yet again, "That's for throwing me in prison!" Shaw released Chuck, dropping him to the floor. Shaw kicked him in the side. Chuck was moaning on the floor in pain. "And that's for my wife!" Shaw finished.

Chuck moaned, the pain was rough.

"But none of that matters anymore; the Ring has fallen, so, when I escaped, I had nowhere to go. All I knew was that I needed revenge, and that's when Christopher Felkin came to me. He explained everything about this world to me, which I'm sure you'll understand soon enough. So, I eagerly joined him, he has taught me many, many things, Chuck; things that you can only dream of. The SMF has given me a much more prestigious position than the CIA, one that I deserve." Spoke Shaw, "Now I am invincible, and you can never defeat me!"

"Wher-" Chuck coughed, "Where's Sarah?" Chuck moaned.

"Ahh, of course," said Shaw, "You two 'love' each other. Pathetic. But no matter, she's in her cell, waiting for me."

"If you touch her!" shouted Chuck.

"Ha! Why?" said Shaw, "It doesn't really matter, since you'll most likely never see her again anyways."

Chuck felt his skin boil. He concentrated for a moment, and flashed. But this flash was different, instead of the usual orange color, it was a dark green. And instead of Martial Arts, as that was what he tried to flash on, it was a bunch of strange symbols. Chuck stood up and charged at Shaw, shoving him into the wall with such force that the wall cracked. Shaw shoved Chuck back, and he fell to the floor with a thud.

"So," said Shaw, unharmed, "the Intersect 3.0 works for you too. I've been getting similar reactions from your friends." Shaw stepped over Chuck, and made his way to the door, which shoot open automatically. "Now it's time that I pay a visit to walker, and don't worry Chuck, I'll take good care of your girlfriend for you." Shaw grinned as he walked away, the door closing. Chuck was still screaming in agony from his flash. Without the Governor, the pain was searing.

Chuck soon felt darkness cloud his vision, as he passed out...


	3. Chuck vs the Philiothramen

Chapter 3: Chuck vs the Philiothramen

Chuck awoke, on the floor of his cell. He rolled over, and found himself underneath his cot. There were strange scratchings and multiple markings engraved into the bottom. He found some English and read it.

_"There are several rules you must maintain if you want to escape, and keep your sanity in the process._

_Rule one: Only use the items hidden in your bed at night. To keep track of time use the mini laptop._

_Rule two: Never lose track of time, one of the ways they make you lose your sanity is by making you lose track of time._

_Rule three: Sleep all day, and stay awake all night. The guards on night duty are much more rowdy, and probably won't pay as much attention to the security monitors._

_Rule four: Make sure that you stay under the bed when using the items, the monitor can't see under the bed."_

Next to Rule One was a slight circular indent. Chuck pushed it in, and a small compartment door fell open on the underside of the bed. Chuck reached in a felt something cold and metallic. He grabbed it and pulled it out. It was a small, mini-laptop.

He reached in again and found a small rucksack, a switchblade, and a long stick. Chuck put the other items back and opened up the rucksack. He removed several of the items and found a diary, a multi-tool army knife, and a wool blanket, amongst some other small things. Then Chuck opened up the diary and began to read it...

Sarah Walker awoke to feeling of pain. Her head was throbbing. She tried to massage her temples, but was unable to move her hands, she noticed that her arms were chained above her head and her ankles were chained to the wall. A few moments later, the door opened, and in walked Daniel Shaw, who bolted the door behind him.

"Ah, Sarah, nice to see your already awake," Said Shaw, "Did Chuck wake you up? That's very rude of him."

"You bastard!" shouted Sarah, "What have you done to my Chuck?"

"Oh, I kicked his ass," said Shaw plainly.

"I'm gonna kill you!" she shouted, struggling at her bonds.

"No need for violence, my dear," said Shaw, stroking a few of Sarah's golden locks.

"Don't touch me!" snapped Sarah, shaking her head.

"Your not really in a position to really do anything about that now are you?" said Shaw with a grin, stroking her cheek with the back of his hand. Sarah struggled in her bonds and attempted to bite his hand.

"But don't worry, Sam, I won't exploit your position...for now," he said with a wink."Right now, you see, I need to test something, would you be so kind as to look at the wall?"

Sarah turned her head and looked at the wall. She saw a strange symbol with the letters SMF written over top of it. To her surprise, she felt her eyes begin to flicker.

_A Spaceship_

_A Picture of a large, futuristic building_

_Recordings of various training exercises_

_Futuristic weapons_

_More training exercises_

_A picture of Daniel Shaw shaking hands with the CEO of the SMF, Christopher Felkin_

_A Spaceship_

She blinked a few times before looking at Shaw again.

"Did I just...flash?" asked Sarah, hiding her fear.

"Yes, my dear, you did," replied Shaw.

"H-How?" she stuttered, her perfect red lips trembling.

"The test we ran on you last night was the Intersect 3.0" said Shaw.

"3.0?" repeated Sarah, "How did you get an Intersect?"

"Made it," said Shaw, "Well, not me, but the SMF technicians did."

"You'll never get away with this!" Shouted Sarah.

"Oh, I will," said Shaw, "And when I do, you will be all mine!"

She spat on his face to show her opinion, "Burn in hell!"

He then kissed her on the lips, hard. Sarah did not return the kiss. He continued to kiss her, attemting to stick his tongue in her mouth. Sarah struggled to break free, but he held her face still. He broke the kiss, and Sarah slammed her head into his.

"You'll regret that!" said Shaw, pulling out a syringe from thin air. "This will only hurt a lot," He said, sticking the needle into her arm, injecting the fluid. The second the fluid entered her bloodstream, she began to feel intense pain. It felt as if her entire body was on fire. She kept screaming, not once asking for mercy. "Had enough?" asked Shaw. She shook her head no. "Very well then, let's see if we can't make time fly, shall we?" he said, producing another syringe and injecting her other arm. The pain doubled, she felt as if she was boiling in hot oil. "I'll just go say 'hi' to your friend Sammy now, I'll be back in a couple of hours, I'll say 'hi' to Chuck for you too."

He left, Sarah still groaning in pain.

Sam had awoken several hours earlier. He was doing chin ups on a bar attached to wall in his cell, when he sensed the presence of Daniel Shaw at his door. Seconds later it creaked open, and he stepped in.

"Well, well, well Sam Williams, at last you are in the rightful custody of the SMF." said Shaw.

"Well, Shaw, since when did you know a thing about me?" Sam asked.

"Oh, I know everything about you," said Shaw with a smile, "You betrayed the SMF.."

"The SMF betrayed _ME_!" yelled Sam, "I never did a thing against the SMF, they have changed, and become evil!"

Shaw, punched at Sam's face, who easily deflected it. He delivered an ax kick to Shaw's face. When Shaw looked at him, Sam could see that he was bleeding.

"You'll pay for that!" shouted Shaw, pulling out his pistol and shooting Sam in the shoulder. Sam screamed in pain and fell to the floor.

"Let's see the legendary Sam Williams, get himself out of this one!" said Shaw, smiling. Just as he finished, the wound began to heal itself. Shaw's smile slowly faded, and Sam's began to grin, as if he sucked Shaw's happiness right out of him. Shaw walked out of the room slamming the door behind him.

Chuck was sitting on his bed when Shaw walked in. He smiled when he saw the mark on his face.

"Did Sarah give you that?" asked Chuck, smiling.

"No, it was that stupid Sam!" said Shaw.

"Huh," said Chuck, "I guess there is a reason to like that kid," He made a mental note to thank him later.

"But, as for Sarah," said Shaw,"I gave two doses of Philiothramen, similar to the one I used in Paris that knocked out her nervous system. This one, however, causes her nervous system more excruciating pain then you could possibly imagine, and that's just one dose, with two I imagine that she broke a while ago."

Chuck tried to control his immense anger, but he couldn't. A flash triggered, martial arts moves flashing in front of his eyes. Despite the immense pain, he was able to focus enough to get one good punch in. The punch made contact with Shaw's jaw. Shaw moaned in pain, spitting out blood. Then, Chuck fell to the ground, screaming in agony, but still satisfied.

"Is that the best you got?" asked Shaw before running out of the room, slamming the door behind him.

As Shaw walked down the hall to room SD-5257-35, Sarah Walker's room, only one thought went through his head: Revenge. He entered the access code to her room: 3-2-7-9-2-4-3-1-Enter. The door opened.

Sarah Walker was still groaning when Shaw walked in. He pulled a syringe out his pocket, this one containing the antidote. He began to speak, even though she had her eyes clenched shut.

"In my hand I hold the antidote the pain your experiencing," said Shaw, "All I need for you to say is that you love me, and will dump that stupid Chuck."

"Never!" said Sarah, still moaning.

Shaw was awe struck, How could she not be broken? The one thing that Shaw didn't know, was that Sarah would definitely not be broken...


End file.
